Skip to content

Pyodide job fails while parsing warning configuration #7783

@lagru

Description

@lagru

It seems that our Emscripten/Pyodide job has started failing all of the sudden. E.g. see this recent failed run on main. I've included the error message below.

Full error message
ERROR: while parsing the following warning configuration:

  ignore:Implicit conversion of A to CSR:scipy.sparse.SparseEfficiencyWarning

This error occurred:

Traceback (most recent call last):
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/numpy/_core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/numpy/_core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/numpy/_core/overrides.py", line 8, in <module>
    from numpy._core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy._core._multiarray_umath'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/numpy/__init__.py", line 114, in <module>
    from numpy.__config__ import show as show_config
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/numpy/__config__.py", line 4, in <module>
    from numpy._core._multiarray_umath import (
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/numpy/_core/__init__.py", line 49, in <module>
    raise ImportError(msg)
ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.12 from "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/bin/python-host-link"
  * The NumPy version is: "2.0.2"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: No module named 'numpy._core._multiarray_umath'


The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/_pytest/config/__init__.py", line 1918, in parse_warning_filter
Warning: ory: type[Warning] = _resolve_warning_category(category_)
                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/_pytest/config/__init__.py", line [195](https://github.com/scikit-image/scikit-image/actions/runs/14672305849/job/41181444607#step:8:196)6, in _resolve_warning_category
    m = __import__(module, None, None, [klass])
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/scipy/__init__.py", line 47, in <module>
    from numpy import __version__ as __numpy_version__
  File "/home/runner/work/scikit-image/scikit-image/.venv-pyodide/lib/python3.12/site-packages/numpy/__init__.py", line 119, in <module>
    raise ImportError(msg) from e
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

Not sure what's causing this and haven't investigated.

Metadata

Metadata

Assignees

No one assigned

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions